# -*- coding: utf-8 -*-
"""
dicom2nifti
@author: abrys
"""
from __future__ import print_function
import dicom2nifti.patch_pydicom_encodings
from dicom2nifti.exceptions import ConversionError
dicom2nifti.patch_pydicom_encodings.apply()
import itertools
import os
from math import pow
import logging
import nibabel
import numpy
from pydicom.tag import Tag
from six import string_types
import dicom2nifti.common as common
import dicom2nifti.convert_generic as convert_generic
logger = logging.getLogger(__name__)
[docs]def dicom_to_nifti(dicom_input, output_file=None):
"""
This is the main dicom to nifti conversion fuction for ge images.
As input ge images are required. It will then determine the type of images and do the correct conversion
Examples: See unit test
:param output_file: the filepath to the output nifti file
:param dicom_input: list with dicom objects
"""
assert common.is_ge(dicom_input)
logger.info('Reading and sorting dicom files')
grouped_dicoms = _get_grouped_dicoms(dicom_input)
if _is_4d(grouped_dicoms):
logger.info('Found sequence type: 4D')
return _4d_to_nifti(grouped_dicoms, output_file)
logger.info('Assuming anatomical data')
return convert_generic.dicom_to_nifti(dicom_input, output_file)
def _is_4d(grouped_dicoms):
"""
Use this function to detect if a dicom series is a ge 4d dataset
NOTE: Only the first slice will be checked so you can only provide an already sorted dicom directory
(containing one series)
"""
# read dicom header
header = grouped_dicoms[0][0]
# check if contains multiple stacks
if len(grouped_dicoms) > 1:
return True
return False
def _is_diffusion_imaging(grouped_dicoms):
"""
Use this function to detect if a dicom series is a ge dti dataset
NOTE: We already assume this is a 4D dataset
"""
# we already assume 4D images as input
# check if contains dti bval information
bval_tag = Tag(0x0043, 0x1039) # put this there as this is a slow step and used a lot
found_bval = False
for header in list(itertools.chain.from_iterable(grouped_dicoms)):
if bval_tag in header and int(header[bval_tag].value[0]) != 0:
found_bval = True
break
if not found_bval:
return False
return True
def _4d_to_nifti(grouped_dicoms, output_file):
"""
This function will convert ge 4d series to a nifti
"""
# Create mosaic block
logger.info('Creating data block')
full_block = _get_full_block(grouped_dicoms)
logger.info('Creating affine')
# Create the nifti header info
affine = common.create_affine(grouped_dicoms[0])
logger.info('Creating nifti')
# Convert to nifti
nii_image = nibabel.Nifti1Image(full_block, affine)
common.set_tr_te(nii_image, float(grouped_dicoms[0][0].RepetitionTime),
float(grouped_dicoms[0][0].EchoTime))
logger.info('Saving nifti to disk %s' % output_file)
# Save to disk
if output_file is not None:
nii_image.to_filename(output_file)
if _is_diffusion_imaging(grouped_dicoms):
bval_file = None
bvec_file = None
# Create the bval en bevec files
if output_file is not None:
base_path = os.path.dirname(output_file)
base_name = os.path.splitext(os.path.splitext(os.path.basename(output_file))[0])[0]
logger.info('Creating bval en bvec files')
bval_file = '%s/%s.bval' % (base_path, base_name)
bvec_file = '%s/%s.bvec' % (base_path, base_name)
bval, bvec = _create_bvals_bvecs(grouped_dicoms, bval_file, bvec_file)
return {'NII_FILE': output_file,
'BVAL_FILE': bval_file,
'BVEC_FILE': bvec_file,
'NII': nii_image,
'BVAL': bval,
'BVEC': bvec
}
return {'NII_FILE': output_file,
'NII': nii_image}
def _get_full_block(grouped_dicoms):
"""
Generate a full datablock containing all timepoints
"""
# For each slice / mosaic create a data volume block
data_blocks = []
for index in range(0, len(grouped_dicoms)):
logger.info('Creating block %s of %s' % (index + 1, len(grouped_dicoms)))
data_blocks.append(_timepoint_to_block(grouped_dicoms[index]))
# Add the data_blocks together to one 4d block
size_x = numpy.shape(data_blocks[0])[0]
size_y = numpy.shape(data_blocks[0])[1]
size_z = numpy.shape(data_blocks[0])[2]
size_t = len(data_blocks)
full_block = numpy.zeros((size_x, size_y, size_z, size_t), dtype=data_blocks[0].dtype)
for index in range(0, size_t):
if full_block[:, :, :, index].shape != data_blocks[index].shape:
logger.warning('Missing slices (slice count mismatch between timepoint %s and %s)' % (index - 1, index))
logger.warning('---------------------------------------------------------')
logger.warning(full_block[:, :, :, index].shape)
logger.warning(data_blocks[index].shape)
logger.warning('---------------------------------------------------------')
raise ConversionError("MISSING_DICOM_FILES")
full_block[:, :, :, index] = data_blocks[index]
return full_block
def _timepoint_to_block(timepoint_dicoms):
"""
Convert slices to a block of data by reading the headers and appending
"""
# similar way of getting the block to anatomical however here we are creating the dicom series our selves
return common.get_volume_pixeldata(timepoint_dicoms)
def _get_grouped_dicoms(dicom_input):
"""
Search all dicoms in the dicom directory, sort and validate them
fast_read = True will only read the headers not the data
"""
# Order all dicom files by InstanceNumber
dicoms = sorted(dicom_input, key=lambda x: x.InstanceNumber)
# now group per stack
grouped_dicoms = [[]] # list with first element a list
stack_index = 0
# loop over all sorted dicoms and sort them by stack
# for this we use the position and direction of the slices so we can detect a new stack easily
previous_position = None
previous_direction = None
for dicom_ in dicoms:
current_direction = None
# if the stack number decreases we moved to the next stack
if previous_position is not None:
current_direction = numpy.array(dicom_.ImagePositionPatient) - previous_position
current_direction = current_direction / numpy.linalg.norm(current_direction)
if current_direction is not None and \
previous_direction is not None and \
not numpy.allclose(current_direction, previous_direction, rtol=0.05, atol=0.05):
previous_position = numpy.array(dicom_.ImagePositionPatient)
previous_direction = None
stack_index += 1
else:
previous_position = numpy.array(dicom_.ImagePositionPatient)
previous_direction = current_direction
if stack_index >= len(grouped_dicoms):
grouped_dicoms.append([])
grouped_dicoms[stack_index].append(dicom_)
return grouped_dicoms
def _get_bvals_bvecs(grouped_dicoms):
"""
Write the bvals from the sorted dicom files to a bval file
"""
# loop over all timepoints and create a list with all bvals and bvecs
bvals = numpy.zeros([len(grouped_dicoms)], dtype=numpy.int32)
bvecs = numpy.zeros([len(grouped_dicoms), 3])
for group_index in range(0, len(grouped_dicoms)):
dicom_ = grouped_dicoms[group_index][0]
# 0019:10bb: Diffusion X
# 0019:10bc: Diffusion Y
# 0019:10bd: Diffusion Z
# 0043:1039: B-values (4 values, 1st value is actual B value)
# bval can be stored both in string as number format in dicom so implement both
# some workarounds needed for implicit transfer syntax to work
if isinstance(dicom_[Tag(0x0043, 0x1039)].value, string_types): # this works for python2.7
original_bval = float(dicom_[Tag(0x0043, 0x1039)].value.split('\\')[0])
elif isinstance(dicom_[Tag(0x0043, 0x1039)].value, bytes): # this works for python3.o
original_bval = float(dicom_[Tag(0x0043, 0x1039)].value.decode("utf-8").split('\\')[0])
else:
original_bval = dicom_[Tag(0x0043, 0x1039)][0]
original_bvec = numpy.array([0, 0, 0], dtype=numpy.float)
original_bvec[0] = -float(dicom_[Tag(0x0019, 0x10bb)].value) # invert based upon mricron output
original_bvec[1] = float(dicom_[Tag(0x0019, 0x10bc)].value)
original_bvec[2] = float(dicom_[Tag(0x0019, 0x10bd)].value)
# Add calculated B Value
if original_bval != 0: # only normalize if there is a value
corrected_bval = original_bval * pow(numpy.linalg.norm(original_bvec), 2)
if numpy.linalg.norm(original_bvec) != 0:
normalized_bvec = original_bvec / numpy.linalg.norm(original_bvec)
else:
normalized_bvec = original_bvec
else:
corrected_bval = original_bval
normalized_bvec = original_bvec
bvals[group_index] = int(round(corrected_bval)) # we want the original numbers back as in the protocol
bvecs[group_index, :] = normalized_bvec
return bvals, bvecs
def _create_bvals_bvecs(grouped_dicoms, bval_file, bvec_file):
"""
Write the bvals from the sorted dicom files to a bval file
"""
# get the bvals and bvecs
bvals, bvecs = _get_bvals_bvecs(grouped_dicoms)
# save the found bvecs to the file
common.write_bval_file(bvals, bval_file)
common.write_bvec_file(bvecs, bvec_file)
return bvals, bvecs